Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes

Abstract

Feline Coronaviruses (FCoVs) commonly cause mild enteric infections in felines worldwide (termed Feline Enteric Coronavirus [FECV]), with around 12% developing into deadly Feline Infectious Peritonitis (FIP; Feline Infectious Peritonitis Virus [FIPV]). Genomic differences between FECV and FIPV have been reported, yet the putative genotypic basis of the highly pathogenic phenotype remains unclear. Here, we used state-of-the-art molecular evolutionary genetic statistical techniques to identify and compare differences in natural selection pressure between FECV and FIPV sequences, as well as to identify FIPV and FECV specific signals of positive selection. We analyzed full length FCoV protein coding genes thought to contain mutations associated with FIPV (Spike, ORF3abc, and ORF7ab). We identified two sites exhibiting differences in natural selection pressure between FECV and FIPV: one within the S1/S2 furin cleavage site, and the other within the fusion domain of Spike. We also found 15 sites subject to positive selection associated with FIPV within Spike, 11 of which have not previously been suggested as possibly relevant to FIP development. These sites fall within Spike protein subdomains that participate in host cell receptor interaction, immune evasion, tropism shifts, host cellular entry, and viral escape. There were 14 sites (12 novel) within Spike under positive selection associated with the FECV phenotype, almost exclusively within the S1/S2 furin cleavage site and adjacent C domain, along with a signal of relaxed selection in FIPV relative to FECV, suggesting that furin cleavage functionality may not be needed for FIPV. Positive selection inferred in ORF7b was associated with the FECV phenotype, and included 24 positively selected sites, while ORF7b had signals of relaxed selection in FIPV. We found evidence of positive selection in ORF3c in FCoV wide analyses, but no specific association with the FIPV or FECV phenotype. We hypothesize that some combination of mutations in FECV may contribute to FIP development, and that is unlikely to be one singular “switch” mutational event. This work expands our understanding of the complexities of FIP development and provides insights into how evolutionary forces may alter pathogenesis in coronavirus genomes.

Feline Infectious Peritonitis: European Advisory Board on Cat Diseases Guidelines

“…Although FCoV infections can undergo a systemic phase within monocytes in healthy cats [ 7 , 8 ], mutations occurring in an individual cat are believed to allow a switch of cell tropism from enterocytes to monocytes to enable the subsequent development of highly pathogenic FIP-inducing FCoV [ 9 ], as discussed later in this review. However, an individual critical mutation has not been identified and likely does not exist [ 10 ].…”

Emergence and spread of feline infectious peritonitis due to a highly pathogenic canine/feline recombinant coronavirus

“…The main determinant in disease development and transmission of FCoV-23 appears to be the spike recombination. One of the main suggested determinants of biotype changes, the furin cleavage site (FCS) at the S1/S2 interface 23,26 is absent in FCoVIIs and also FCoV-23. An interesting observation, however, is that the majority of samples show a deletion in domain 0, strongly resembling the deletion observed in TGEV and porcine respiratory coronavirus (PRCV) (Figure 4A).…”

“…Clinical signs include an abdomen swollen due to peritoneal fluid, fever, weight loss lethargy, anorexia, dyspnoea, ocular abnormalities and neurological signs 8,16,24,25 . Mutations in the spike gene or the accessory genes 3abc and of 7ab of FCoV 8,16,23,26 are thought to result in changes to the virus’s tropism from cells in the enteric tract to macrophages, resulting in the different disease presentation seen with the two biotypes. This change in primary tropism also impacts the virus’s ability to transmit from cat to cat, with the main transmission pathway of FECV being faecal-oral and FIPV typically having relatively poor transmission potential.…”

“…Multi-sequence alignment was performed against four confirmed FECV-2 and four confirmed FIPV-2 mirroring sequences used for computational analysis by Zehr et al . 26 . Highlighted are amino acid changes with significant change against FCoVIIs and also position 546, where a Leucin is more predominant in FIPV rather than FECV sequences.…”

“…Previously indicated key proteins for biotype switch spike, Orf3abc and 7b were compared to the recently published computational analysis of mutations observed in FECV versus FIPV by Zehr et al . 26 . Unfortunately, the suggested key determinant of FIPV in the FCoV-2 spike, position 1404, is not yet resolved in FCoV-23.…”